Introduction
Protein Structure
&
Molecular Modelling
Version 1.5
BIOSCIENCE IT SERVICES
Molecular Biology Support
Scientific Applications Section
BBSRC Bioscience IT Services
Harpenden, Herts
AL5 2JE
e-mail: molbio.support@bbsrc.ac.uk
Tel : 01582 714 904
Fax : 01582 714 901
February 2004
Introduction
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Copyright \u00a9 Bioscience IT Services 2001
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3
1. Introduction
8
Abbreviations
8
Useful Information
9
Groups of amino acids
10
Bond Geometry
10
Keyboard Shortcuts in Deep View
11
Introduction to the course
12
Course summary
12
Hardware and Software requirements
12
Deep View version 3.72
13
Getting Help
13
Presentation Slides
14
2. Fetching and understanding protein structure files
20
The Protein Databank (PDB)
20
Searching for PDB files
21
Accession code
21
Text searching
22
The PDB annotation page
25
Summary Page
25
Data Retrieval
27
Viewing the structure
27
Analysing a PDB file
29
3. Viewing and analysing structures in Deep View
31
What is Deep View?
31
How can I get Deep View?
31
Configuring Deep View
32
General Preferences (Preferences\u2192 General)
33
Loading Preferences (Preferences\u2192 Loading Protein)
33
Swiss Model Preferences (Preferences\u2192 Swiss-Model)
34
Network Preferences (Preferences\u2192 Network)
34
Help
35
Viewing and manipulating a structure
36
Importing a molecule
36
Loading a molecule
36
Initial view
37
Moving around the molecule
37
Changing the view of the molecule
39
Layers Infos Window
41
Control Panel
42
The Header
42
Group List
42
Colours
44
Changing attributes
46
View Mode
47
Changing how the molecule is displayed
49
Slab mode
49
Exercises for changing the view of a molecule
50
Selecting Groups
52
None / All
52
Inverse selection
52
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